Back to Build/check report for BioC 3.17
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This page was generated on 2023-02-08 01:15:25 -0000 (Wed, 08 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4164
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CHECK results for RnBeads on kunpeng1


To the developers/maintainers of the RnBeads package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RnBeads.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1698/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads 2.17.0  (landing page)
Fabian Mueller
Snapshot Date: 2023-02-06 00:12:45 -0000 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/RnBeads
git_branch: master
git_last_commit: 99cf51e
git_last_commit_date: 2023-01-03 12:42:18 -0000 (Tue, 03 Jan 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    ERROR  

Summary

Package: RnBeads
Version: 2.17.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RnBeads_2.17.0.tar.gz
StartedAt: 2023-02-07 13:45:39 -0000 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 13:57:57 -0000 (Tue, 07 Feb 2023)
EllapsedTime: 738.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: RnBeads.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RnBeads_2.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RnBeads.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘2.17.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster',
  'ff', 'fields', 'ggplot2', 'gplots', 'grid', 'gridExtra', 'limma',
  'matrixStats', 'illuminaio', 'methylumi', 'plyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RnBeads’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     3.1Mb
    bin   1.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘qvalue’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Killed
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Killed
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘RnBeads-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rnb.execute.pOOBAH
> ### Title: rnb.execute.pOOBAH
> ### Aliases: rnb.execute.pOOBAH
> 
> ### ** Examples
> 
> library(RnBeads.hg19) 
> data(small.example.object)
> filtered <- rnb.execute.pOOBAH(rnb.set.example)
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  2023-02-07 13:54:58     1.4  STATUS                 STARTED Computing Differential Methylation Table
  2023-02-07 13:54:58     1.4    INFO                     Conducting differential analysis using limma
  2023-02-07 13:54:58     1.4  STATUS                 COMPLETED Computing Differential Methylation Table
  2023-02-07 13:54:58     1.4  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
  2023-02-07 13:55:00     1.4  STATUS                     Computed table for tiling
  2023-02-07 13:55:00     1.4  STATUS                     Computed table for genes
  2023-02-07 13:55:00     1.4  STATUS                     Computed table for promoters
  2023-02-07 13:55:00     1.4  STATUS                     Computed table for cpgislands
  2023-02-07 13:55:00     1.4  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
  2023-02-07 13:55:00     1.4  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
  2023-02-07 13:55:00     1.4  STATUS         COMPLETED Computing differential methylation tables
  2023-02-07 13:55:00     1.4  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
  2023-02-07 13:55:00     1.4  STATUS     STARTED Testing function: diffVar
  2023-02-07 13:55:01     1.4  STATUS         STARTED diffVar method
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘RnBeads.Rnw’... failed to complete the test
  ‘RnBeads_Annotations.Rnw’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘RnBeads.Rnw’
  ...
8  hiPS_17b_p35_TeSR   hiPS_17b     TRUE
9       hiPS_27b_p31   hiPS_27b     TRUE
10    hES_HUES64_p19 hES_HUES64    FALSE
11 hiPS_17b_p35_KOSR   hiPS_17b     TRUE
12        hES_H9_p58     hES_H9    FALSE

> Mint <- M(rnb.set.example, row.names = TRUE)
Killed

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/RnBeads.Rcheck/00check.log’
for details.


Installation output

RnBeads.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RnBeads
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘RnBeads’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RnBeads)

Tests output

RnBeads.Rcheck/tests/runTests.Rout.fail


R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("RnBeads")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'bit'

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="/tmp/RtmpgXZSnO/ff"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

The following objects are masked from 'package:utils':

    write.csv, write.csv2

The following objects are masked from 'package:base':

    is.factor, is.ordered

Spam version 2.9-1 (2022-08-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following object is masked from 'package:stats4':

    mle

The following objects are masked from 'package:base':

    backsolve, forwardsolve


Try help(fields) to get started.

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess


Attaching package: 'grid'

The following object is masked from 'package:ff':

    pattern


Attaching package: 'gridExtra'

The following object is masked from 'package:BiocGenerics':

    combine


Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'scales'

The following object is masked from 'package:viridis':

    viridis_pal


Attaching package: 'AnnotationDbi'

The following object is masked from 'package:MASS':

    select



Attaching package: 'MatrixGenerics'

The following object is masked from 'package:Biobase':

    rowMedians

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars


Attaching package: 'Biostrings'

The following object is masked from 'package:grid':

    pattern

The following objects are masked from 'package:ff':

    mismatch, pattern

The following object is masked from 'package:base':

    strsplit

locfit 1.5-9.7 	 2023-01-02
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'plyr'

The following object is masked from 'package:XVector':

    compact

The following object is masked from 'package:matrixStats':

    count

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

2023-02-07 13:54:51     1.1  STATUS STARTED Unit testing: differential
2023-02-07 13:54:51     1.1  STATUS     STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2023-02-07 13:54:51     1.1  STATUS     COMPLETED Testing function: rowWelchP
2023-02-07 13:54:51     1.1  STATUS     STARTED Testing function: limmaP
2023-02-07 13:54:51     1.1  STATUS     COMPLETED Testing function: limmaP
2023-02-07 13:54:51     1.1  STATUS     STARTED Testing function: computeDiffTab.extended.site
2023-02-07 13:54:51     1.1    INFO         Conducting differential analysis using limma
2023-02-07 13:54:51     1.1  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2023-02-07 13:54:51     1.1  STATUS     STARTED Testing function: computeDiffTab.default.region
2023-02-07 13:54:52     1.1    INFO         Conducting differential analysis using limma
2023-02-07 13:54:56     1.2  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2023-02-07 13:54:56     1.2  STATUS     STARTED Testing function: combineTestPvalsMeth
2023-02-07 13:54:56     1.2  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2023-02-07 13:54:56     1.2  STATUS     STARTED Testing function: get.adjustment.variables
2023-02-07 13:54:56     1.2  STATUS     COMPLETED Testing function: get.adjustment.variables
2023-02-07 13:54:56     1.2  STATUS     STARTED Testing function: get.comparison.info
2023-02-07 13:54:56     1.2  STATUS     COMPLETED Testing function: get.comparison.info
2023-02-07 13:54:56     1.2  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2023-02-07 13:54:56     1.2  STATUS         STARTED Retrieving comparison info
2023-02-07 13:54:56     1.2  STATUS         COMPLETED Retrieving comparison info
2023-02-07 13:54:56     1.2  STATUS         STARTED Computing differential methylation tables
2023-02-07 13:54:56     1.2  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-02-07 13:54:56     1.2  STATUS                 STARTED Computing Differential Methylation Table
2023-02-07 13:54:56     1.2    INFO                     Conducting differential analysis using limma
2023-02-07 13:54:56     1.2  STATUS                 COMPLETED Computing Differential Methylation Table
2023-02-07 13:54:56     1.2  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2023-02-07 13:54:57     1.3  STATUS                     Computed table for tiling
2023-02-07 13:54:57     1.4  STATUS                     Computed table for genes
2023-02-07 13:54:57     1.4  STATUS                     Computed table for promoters
2023-02-07 13:54:58     1.4  STATUS                     Computed table for cpgislands
2023-02-07 13:54:58     1.4  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2023-02-07 13:54:58     1.4  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-02-07 13:54:58     1.4  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-02-07 13:54:58     1.4  STATUS                 STARTED Computing Differential Methylation Table
2023-02-07 13:54:58     1.4    INFO                     Conducting differential analysis using limma
2023-02-07 13:54:58     1.4  STATUS                 COMPLETED Computing Differential Methylation Table
2023-02-07 13:54:58     1.4  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2023-02-07 13:55:00     1.4  STATUS                     Computed table for tiling
2023-02-07 13:55:00     1.4  STATUS                     Computed table for genes
2023-02-07 13:55:00     1.4  STATUS                     Computed table for promoters
2023-02-07 13:55:00     1.4  STATUS                     Computed table for cpgislands
2023-02-07 13:55:00     1.4  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2023-02-07 13:55:00     1.4  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-02-07 13:55:00     1.4  STATUS         COMPLETED Computing differential methylation tables
2023-02-07 13:55:00     1.4  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2023-02-07 13:55:00     1.4  STATUS     STARTED Testing function: diffVar
2023-02-07 13:55:01     1.4  STATUS         STARTED diffVar method
Killed

Example timings

RnBeads.Rcheck/RnBeads-Ex.timings

nameusersystemelapsed
M-methods000
U-methods0.0000.0000.001
addDiffMethTable-RnBDiffMeth-methods000
addPheno-RnBSet-methods000
addRegionSubsegments000
annotation-methods000
assembly-methods000
combine.rnb.sets-methods000
combineTestPvalsMeth0.0000.0000.001
computeDiffTab.region000
computeDiffTab.site000
covg-methods000
create.densityScatter000
create.scatter.dens.points000
createReport000
createReportPlot000
downloadLolaDbs000
dpval-methods000
exportDMRs2regionFile000
get.adjustment.variables000
get.comparison.grouplabels-RnBDiffMeth-methods000
get.comparison.groupsizes-RnBDiffMeth-methods0.0000.0000.001
get.comparison.info000
get.comparisons-RnBDiffMeth-methods000
get.covariates.sva0.0000.0000.001
get.covg.thres-RnBDiffMeth-methods000
get.files000
get.region.types-RnBDiffMeth-methods000
get.site.test.method-RnBDiffMeth-methods000
get.table-RnBDiffMeth-methods000
getCellTypesFromLolaDb000
getNamesFromLolaDb000
getSubCmdTokens-ClusterArchitectureSGE-methods000
getSubCmdTokens-ClusterArchitectureSLURM-methods000
getTargetFromLolaDb000
has.covariates.sva000
hasCovg-methods000
includes.sites-RnBDiffMeth-methods0.0000.0000.001
is.valid-RnBDiffMeth-methods000
join.diffMeth-methods000
limmaP000
loadLolaDbs000
logger.argument000
logger.getfiles000
logger.isinitialized000
logger.validate.file000
loggerManagement000
loggerMessages000
lolaBarPlot000
lolaBoxPlotPerTarget000
lolaVolcanoPlot000
mergeSamples-methods000
meth-methods000
mval-methods000
nsites-methods000
parallel.getNumWorkers000
parallel.isEnabled000
parallel.setup000
parallel.teardown000
performGOEnrichment.diffVar000
performGOenrichment.diffMeth.entrez000
performGoEnrichment.diffMeth000
performLolaEnrichment.diffMeth000
performLolaEnrichment.diffVar000
pheno-methods000
qc-methods000
read.sample.annotation000
regionMapping-methods000
regions-methods000
reload-RnBDiffMeth-methods000
remove.regions-methods000
remove.samples-methods000
remove.sites-methods000
rnb.RnBSet.to.GRangesList000
rnb.RnBSet.to.bed000
rnb.RnBSet.to.bedGraph000
rnb.add.list000
rnb.add.paragraph000
rnb.add.reference000
rnb.add.section000
rnb.annotation.size000
rnb.annotation2data.frame000
rnb.beta2mval000
rnb.execute.batcheffects000
rnb.execute.clustering000
rnb.execute.computeDiffMeth000
rnb.execute.context.removal000
rnb.execute.cross.reactive.removal000
rnb.execute.dreduction000
rnb.execute.export.csv000
rnb.execute.greedycut000
rnb.execute.import000
rnb.execute.na.removal000
rnb.execute.normalization000